• Molecules and Cells
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• v.27 no.3
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• pp.329-336
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• 2009

To evaluate the involvement of translation initiation factors eIF4E and eIFiso4E in Chilli veinal mottle virus (ChiVMV) infection in pepper, we conducted a genetic analysis using a segregating population derived from a cross between Capsicum annuum 'Dempsey' containing an elF4E mutation ($pvr1^2$) and C. annuum 'Perennial' containing an elFiso4E mutation (pvr6). C. annuum 'Dempsey' was susceptible and C. annuum 'Perennial' was resistant to ChiVMV. All $F_1$ plants showed resistance, and $F_2$ individuals segregated in a resistant-susceptible ratio of 166:21, indicating that many resistance loci were involved. Seventy-five $F_2$ and 329 $F_3$ plants of 17 families were genotyped with $pvr1^2$ and pvr6 allele-specific markers, and the genotype data were compared with observed resistance to viral infection. All plants containing homozygous genotypes of both $pvr1^2$ and pvr6 were resistant to ChiVMV, demonstrating that simultaneous mutations in elF4E and eIFiso4E confer resistance to ChiVMV in pepper. Genotype analysis of $F_2$ plants revealed that all plants containing homozygous genotypes of both $pvr1^2$ and pvr6 showed resistance to ChiVMV. In protein-protein interaction experiments, ChiVMV viral genome-linked protein (VPg) interacted with both eIF4E and eIFiso4E. Silencing of elF4E and eIFiso4E in the VIGS experiment showed reduction in ChiVMV accumulation. These results demonstrated that ChiVMV can use both eIF4E and eIFiso4E for replication, making simultaneous mutations in eIF4E and eIFiso4E necessary to prevent ChiVMV infection in pepper.

• 한국균학회소식:학술대회논문집
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• 2014.10a
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• pp.13-13
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• 2014

Species belonging to the genus Fusarium are widely distributed and cause diseases in many plants. Isolation of fungal strains from air or cereals is necessary for disease forecasting, disease diagnosis, and population genetics [1]. Previously we showed that Fusarium species are resistant to toxoflavin produced by the bacterial rice pathogen Burkholderia glumae while other fungal genera are sensitive to the toxin, resulting in the development of a selective medium for Fusarium species using toxoflavin [2]. In this study, we have tried to elucidate the resistant mechanism of F. graminearum against toxoflavin and interaction between the two pathogens in nature. To test whether B. glumae affects the development of F. graminearum, the wild-type F. graminearum strains were incubated with either the bacterial strain or supernatant of the bacterial culture. Both conditions increased the conidial production five times more than when the fungus was incubated alone. While co-incubation resulted in dramatic increase of conidial production, conidia germination delayed by either the bacterial strain or supernatant. These results suggest that certain factors produced by B. glumae induce conidial production and delay conidial germination in F. graminearum. To identify genes related to toxoflavin resistance in F. graminearum, we screened the transcriptional factor mutant library previously generated in F. graminearum [3] and identified one mutant that is sensitive to toxoflavin. We analyzed transcriptomes of the wild-type strain and the mutant strain under either absence or presence of toxoflavin through RNAseq. Expression level of total genes of 13,820 was measured by reads per kilobase per million mapped reads (RPKM). Under the criteria with more than two-fold changes, 1,440 genes were upregulated and 1,267 genes were down-regulated in wild-type strain than mutant strain in response to toxoflavin treatment. A comparison of gene expression profiling between the wild type and mutant through gene ontology analysis showed that genes related to metabolic process and oxidation-reduction process were highly enriched in the mutant strain. The data analyses will focus on elucidating the resistance mechanism of F. graminearum against toxoflavin and the interaction between the two pathogens in rice. Further evolutionary history will be traced through figuring out the gene function in populations and in other filamentous fungi.

• Clinical and Experimental Reproductive Medicine
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• v.38 no.3
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• pp.168-173
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• 2011

Objective: To examine the association between methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and hyperhomocysteinemia in women with unexplained recurrent miscarriages (RM) and to investigate the association between MTHFR genotype variants and alloimmune activation, proportion of peripheral blood natural killer (pbNK) cells. Methods: A total of 39 patients with a history of two or more unexplained miscarriages were recruited to this study. The controls were women who had a live birth without a history of RM (n=50). The proportion of pbNK cells was measured by flow cytometry. Plasma homocysteine levels and the incidence of the MTHFR variant of the RM and control groups were compared. The proportion of pbNK cells was compared to the MTHFR variants in the RM group. Results: No differences were found between the two groups' mean plasma homocysteine levels ($7.6{\pm}1.5{\mu}mol$/L vs. $7.1{\pm}2.1{\mu}mol$/L) or incidence of the MTHFR genotype variant (CC, 35% vs. 33%; CT, 40% vs. 53%; and TT, 25% vs. 14%). In the RM group, individuals with the TT variant ($7.7{\pm}1.1{\mu}mol$/L) had higher homocysteine levels than those with the CC and CT variants ($7.4{\pm}1.9{\mu}mol$/L and $7.4{\pm}1.2{\mu}mol$/L) and those with the CT variant ($19.2{\pm}8.1%$) had a higher proportion of CD3-/CD56+ pbNK cells than those with the CC and TT variants ($17.7{\pm}6.6%$ and $17.9{\pm}7.0%$), but the results of both comparisons were statistically insignificant. Conclusion: These preliminary results show no difference in plasma homocysteine levels between the RM and control groups or among MTHFR genotype variants in the RM group, which may suggest that the plasma homocysteine level is difficult to use as a predictive marker of RM in the Korean population. A study of a larger number of patients is needed.

• Animal Systematics, Evolution and Diversity
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• v.18 no.1
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• pp.13-21
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• 2002

To add genetic information to the conservation efforts on grey coral (Naemorhedus caudatus) in Korea, we investigated the pattern of mitochondrial cytochrome b gene sequence (606 bp) of six specimens from two localities in Korea. The corresponding sequences of N. caudatus in China obtained from GenBank were also used. The nucleotide Tamura-Nei distances between each of four haplotypes of N. caudatus in Korea and the haplotype of N. caudatus in China varied from 0.0650 to 0.0803: N. caudatus revealed high level of sequence diversity in Bovidae. In N. caudatus in Korea, the distances among three haplotypes at Yanggu were 0.0151 to 0.0185, and it suggests that the genetic diversity of Yanggu population was decreased in low level. Moreover, the distances between each of three haplotypes at Yanggu and one haplotype at Samcheok were 0.0343 to 0.0489. It indicates that habitat isolation caused the continuous increase of genetic distance with geographic distance in N. caudatus, and various conservation plans for mitigating the loss of genetic diversity in Korea have to be in immediate action. To clarify the taxonomic status of N. caudatus, the sequence (276 bp) of N. goral available from GenBank were also utilized, and n goral was not distinct from N. caudatus. It suggests that they may be conspecific, but further analyses with additional specimens of two species are necessary.

• Genomics & Informatics
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• v.14 no.2
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• pp.62-68
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• 2016

Osteoporosis is a medical condition of global concern, with increasing incidence in both sexes. Bone mineral density (BMD), a highly heritable trait, has been proven a useful diagnostic factor in predicting fracture. Because medical information is lacking about male osteoporotic genetics, we conducted a genome-wide association study of BMD in Korean men. With 1,176 participants, we analyzed 4,414,664 single nucleotide polymorphisms (SNPs) after genomic imputation, and identified five SNPs and three loci correlated with bone density and strength. Multivariate linear regression models were applied to adjust for age and body mass index interference. Rs17124500 ($p=6.42{\times}10^{-7}$), rs34594869 ($p=6.53{\times}10^{-7}$) and rs17124504 ($p=6.53{\times}10^{-7}$) in 14q31.3 and rs140155614 ($p=8.64{\times}10^{-7}$) in 15q25.1 were significantly associated with lumbar spine BMD (LS-BMD), while rs111822233 ($p=6.35{\times}10^{-7}$) was linked with the femur total BMD (FT-BMD). Additionally, we analyzed the relationship between BMD and five genes previously identified in Korean men. Rs61382873 (p = 0.0009) in LRP5, rs9567003 (p = 0.0033) in TNFSF11 and rs9935828 (p = 0.0248) in FOXL1 were observed for LS-BMD. Furthermore, rs33997547 (p = 0.0057) in ZBTB and rs1664496 (p = 0.0012) in MEF2C were found to influence FT-BMD and rs61769193 (p = 0.0114) in ZBTB to influence femur neck BMD. We identified five SNPs and three genomic regions, associated with BMD. The significance of our results lies in the discovery of new loci, while also affirming a previously significant locus, as potential osteoporotic factors in the Korean male population.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.6
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• pp.3015-3020
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• 2016

Background: Numerous studies have investigated associations of DNA methyltransferase (DNMT) -149 C>T and -579 G>T polymorphisms with gastric cancer (GC) and colorectal cancer (CRC) susceptibility; however, the findings are inconsistent prompting the present meta-analysis. Materials and Methods: Related studies were identified from PubMed, Google scholar, and SID until 10 October 2015. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strength of the associations. Results: Eleven studies were included based on the search criteria for CRC and GC related to the DNMT3B 149 C>T (3,353 cases and 4,936 controls) and DNMT3B 579 G>T (1,387 cases and 2,064 controls) polymorphisms. There was no significant association overall between DNMT3B -149 and 579 polymorphisms and the risk of cancer. In the stratified analysis by cancer type, DNMT3B 579G>T polymorphism was associated with the risk of CRC and GC. While the DNMT3B -149C/T polymorphism was related with a significantly increased risk of CRC in two tested models, dominant (GG+GT vs. TT: OR 0.51, 95 % CI 0.38-0.69; P = 0.00, Pheterogeneity=0.69, $I^2=0%$) and heterozygote (GT vs. TT: OR 0.50, 95 % CI 0.37-0.69; P=0.00, Pheterogeneity=0.41, $I^2=0%$), no evidence of any association with GC risk was observed as in the pooled analyses. Conclusions: More studies are needed to assess associations of DNMT3B -149C/T and DNMT3B 579G>T polymorphisms with cancer in different ethnicities with large population sizes to generate comprehensive conclusions.

• Genes and Genomics
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• v.40 no.12
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• pp.1373-1382
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• 2018

Hanwoo and Chikso are classified as Korean native cattle breeds that are currently registered with the Food and Agriculture Organization. However, there is still a lack of genomic studies to compare Hanwoo to Chikso populations. The objective of this study was to perform genome-wide analysis of Hanwoo and Chikso populations, investigating the genetic relationships between these two populations. We genotyped a total of 319 cattle including 214 Hanwoo and 105 Chikso sampled from Gangwon Province Livestock Technology Research Institute, using the Illumina Bovine SNP50K Beadchip. After performing quality control on the initially generated datasets, we assessed linkage disequilibrium patterns for all the possible SNP pairs within 1 Mb apart. Overall, average $r^2$ values in Hanwoo (0.048) were lower than Chikso (0.074) population. The genetic relationship between the populations was further assured by the principal component analysis, exhibiting clear clusters in each of the Hanwoo and Chikso populations, respectively. Overall heterozygosity for Hanwoo (0.359) was slightly higher than Chikso (0.345) and inbreeding coefficient was also a bit higher in Hanwoo (-0.015) than Chikso (-0.035). The average $F_{ST}$ value was 0.036 between Hanwoo and Chikso, indicating little genetic differentiation between those two breeds. Furthermore, we found potential selection signatures including LRP1B and NTRK2 genes that might be implicated with meat and reproductive traits in cattle. In this study, the results showed that both Hanwoo and Chikso populations were not under severe level of inbreeding. Although the principal component analysis exhibited clear clusters in each of the populations, we did not see any clear evidence that those two populations are highly differentiated each other.

• Korean Journal of Breeding Science
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• v.43 no.5
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• pp.464-469
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• 2011

Virus diseases often cause serious damage to rice production in Asia. The lack of information on virus resistance genes has been a major obstacle for the breeding of resistant varieties. In order to identify DNA marker associated with resistance against rice stripe virus (RSV), the quantitative trait locus (QTL) was carried out using advanced backcross population developed from a cross between RSV-resistant tongil type cultivar Shinkwang and susceptible japonica cultivar Ilpum. A RSV resistance QTL $qSTV11^{SG}$ explaining 44.2% of the phenotypic variation was identified on chromosome 11 of Tongil type rice cultivar 'Shingwang'. $qSTV11^{SG}$ was tightly linked to DNA marker RM6897. The RM6897 divided as resistance type allele and susceptible type alleles. Twenty seven resistant varieties showed the resistant-type allele and 23 susceptible varieties were susceptible-type allele to the marker of RM6897. This results and the molecular markers presented here may be useful in rice breeding for improving RSV resistance in japonica rice.

• Fisheries and Aquatic Sciences
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• v.27 no.3
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• pp.180-194
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• 2024

Mass mortalities of mud crab Scylla spp. larvae due to pathogenic Vibrio spp. outbreaks have frequently occurred in hatcheries. To overcome this problem, probiotics containing Bacillus subtilis bacteria are applied to inhibit pathogenic ones. We tested different doses of probiotic-containing B. subtilis (10⁸ CFU/g) on the Scylla tranquebarica larvae and investigated the microbiota population, including Vibrio. Water quality, larvae development, and crablet production were also monitored. The recently hatched larvae were grown in twelve conical fiber tanks filled with 200 L sterile seawater, with a salinity of 30 ppt at a stocking density of 80 ind/L. Four different doses of probiotics were applied in the larvae rearing, namely, A = 2.5 mg/L, B = 5 mg/L, C = 7.5 mg/L, and D = 0 mg/L, with three replicates. Next-generation sequencing analysis was used to obtain the abundance of microbes in the whole body of megalopa and the water media for larvae rearing after applying probiotics. Sixteen Raw Deoxyribonucleic Acid samples (eight from a whole body of megalopa extraction from four treatments of probiotics defined as A, B, C, D, and eight from water media extraction from four treatments of probiotic defined as E, F, G, H) were prepared. Then, they were sent to the Genetics Science Laboratory for NGS analysis. Ammonia, nitrite, total organic matter (TOM), larvae, and crablet production were monitored. Based on the Next-generation sequencing analysis data, the Vibrio spp. decreased significantly (p < 0.05) than control test (D) in megalopa-applied probiotics at the doses of 2.5 mg/L (A) and 7.5 mg/L (C) and in the water media for megalopa rearing treated with probiotics at the dosage of 5.0 mg/L (F). Ammonia in the zoea stage in B treatment and TOM in the zoea and megalopa stage in B and C treatments were decreased significantly (p < 0.05). It impacts the higher number of zoea survival in treatments B and C. Finally, it results in a significantly high crablet production in treatments B and C. Therefore, the dosage of 5 mg/L to 7.5 mg/L improves crablet S. tranquebarica production significantly.

• Journal of Plant Biology
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• v.3 no.2
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• pp.6-18
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• 1960

The present experiments were designed in order to clarify the differences between the long and short styled plants and the transgressive gradition in the degree of dimorphism among the three heterostylous species of the Polygonus, P. japonica, F. esculentum, and P. senticosa, based on investigations regarding the floral structure, ecological and physiological traits, the results of which are summarized as follows: (1) P. japonica, although it exhibits typical dimorphism, has undergone so high a differentiation between long and short styled that its long styled individuals behave as if they were female; and short styled individuals as if male. In long-styled individuals, filament, anther, and pollen grains show signs of degeneration, most of the pollen being abortive. On the other hand, in short styled individuals, the filament, anther, and pollen grains have attained remarkable development; the pollen grians are large and fertile. In short-plant the fertilized flowers readily drop off in every stage of their embryo development. This species has completely lost the self-fertile property, which is characteristic of the non-dimorphic Polygonum genus. Although this specsei typically exhibits the physiological characteristics of the non-dimorphic Polygonum genus. Although this specisei typically exhibits the physiological characteristics of dimorphism in controlled pollination, the short-styled individuals bear no seed in nature, thus misleading taxonomists to idenfity the short-styled plant as male. 2) The morphological feature of the flower organ of P. senticosa obviously indicates definite dimorphism. Physiologically, however, no differentiation towards dimorphism was observed, the species still retaining, both in long and short-individuals, the self-fertile property common to the Polygonum genus. Elaborate examinations revealed that regardless of the modes of pollination, both fertiization and seed setting flourish, no differentiation betwen legitimate and illegitimate unions being recognizable. This sort of physiological property has not been observed in the investigations of other heterostylous plants. It is assumed that this species is differentiated structurally into dimorphism, but not yet physiologically. In nature, however, this plant would have more opportunities to be cross-pollinated, i.e., legitimately combined, than self-pollinated because of the development of two forms of flowers. 3) In terms of heterostylism, the F. esculentum just occupies the intermediate position between P. japonica and P. senticosa structurally, ecologically, and physiologically. Doescription of some of the physiological behavior of the plant will suffice to demonstrate the above facts. While P. japonica has completely lost its self-fertile property, P. senticosa still retains it wolly. In F. esculentum 2-6% of self-fertility is the result in illegitimate combination. There occur occasionally hereditary self fertile individuals among some of the F. or 20 min. irradiation plot, when they reach any stage of the same bacterial population. In addition to this increase of total population in the plots with the more dose of UV light irradiation, it seems that the more dose of UV light irradiation is the more shortened the generation time of Azotobacter. Therefore, it is clear that variation of reproductive rate must be, mere or less, due to the genetic effects induced by UV light irradiation. On the other hand, the lag phase or logarithmic growth phase in nonirradiated culture is shortened prominently, and this must be due to the difference in bacterial number of the original inoculm. The generation time of Azotobacter is shortened by exogeneous treatment of nuclei acid derivatives, and the degree is greater in case of DNA derivatives than RNA dervatives. W.H. Price reported that the rate of ribose nucleic acid to protein in Staphylococcus muscae is proportional to the generation time: that is the faster the cell can form ribose nucleic acid, the more rapid its growth. This explains the shortening of generation time by exogeneous RNA derivatives in this work reasonably. On the other hand, it is well known that the desoxyribose nuclic acid content per cell is constant and independent of the generation time. A.D. Laren and W.N. Takahashi reported that the infectious RNA from TMV is 6 times as sensitive to inactivation by UV as it is in the form of intact virus, and that inactivation of infectious TMV involves onlu a local change on RNA chain. But, the effect of exogeneous DNA in this work suggests that irradiated living cell which cotain DNA bring about some change on DNA moleculs as well as RNA molecules. And if the mutagenic effects of UV take into consideration, it is very reasonable. Therefore, it is clear that the variation of the generation time by UV irradiation is, more or less, due to the genetic effects. Therefore, it seems that the shortness of the average lifewpan of Azotobacter by UV irradiation is resulted not only from the influence of the environmental conditions, but also from the variation of genetic factor of the individual.